NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P40636 UniProt NPD GO	ADW5_ALLMI	SRY-related protein ADW5 (Fragment)	0.46	-	nuc	0	Nucleus (Potential)				72
O95630 UniProt NPD GO	STABP_HUMAN	STAM-binding protein (EC 3.1.2.15) (Associated molecule with the SH3 domain of STAM)	0.46	-	nuc	0	Nucleus. Membrane; peripheral membrane. Cytoplasm	nucleus [TAS]	606247		424
Q9U4F3 UniProt NPD GO	SURF1_DROME	SURF1-like protein	0.46	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [ISS]			300
Q9IA96 UniProt NPD GO	SFRP2_CHICK	Secreted frizzled-related protein 2 precursor (sFRP-2)	0.46	+	exc	0	Secreted protein (By similarity)				292
Q9JJX8 UniProt NPD GO	ST32B_MOUSE	Serine/threonine-protein kinase 32B (EC 2.7.11.1)	0.46	-	nuc	0					414
P43568 UniProt NPD GO	CAK1_YEAST	Serine/threonine-protein kinase CAK1 (EC 2.7.11.22) (CDK-activating kinase)	0.46	-	cyt	0		cytoplasm [IDA]			368
Q05609 UniProt NPD GO	CTR1_ARATH	Serine/threonine-protein kinase CTR1 (EC 2.7.11.1)	0.46	-	nuc	0					821
Q8CIN4 UniProt NPD GO	PAK2_MOUSE	Serine/threonine-protein kinase PAK 2 (EC 2.7.11.1) (p21-activated kinase 2) (PAK-2)	0.46	-	nuc	0					524
Q28651 UniProt NPD GO	2A5G_RABIT	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform (PP2A, B subunit, B' ...	0.46	-	nuc	0	Nucleus (By similarity)				524
Q8R4Z1 UniProt NPD GO	SPA12_RAT	Serpin A12 precursor (Visceral adipose-specific serpin) (Visceral adipose tissue-derived serine prot ...	0.46	-	cyt	0	Secreted protein (Potential)				411
P19121 UniProt NPD GO	ALBU_CHICK	Serum albumin precursor (Alpha-livetin) (Allergen Gal d 5)	0.46	-	mit	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			615
Q9QX01 UniProt NPD GO	TRPC1_RAT	Short transient receptor potential channel 1 (TrpC1) (TRP-1 protein) (Trp1)	0.46	-	end	6	Membrane; multi-pass membrane protein				759
Q9Y286 UniProt NPD GO	SIGL7_HUMAN	Sialic acid-binding Ig-like lectin 7 precursor (Siglec-7) (QA79 membrane protein) (Adhesion inhibito ...	0.46	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604410	2G5R	467
Q64393 UniProt NPD GO	NEUR2_CRIGR	Sialidase-2 (EC 3.2.1.18) (Cytosolic sialidase) (N-acetyl-alpha-neuraminidase 2)	0.46	-	cyt	0	Cytoplasm (By similarity)				379
Q6BM93 UniProt NPD GO	SEC65_DEBHA	Signal recognition particle SEC65 subunit	0.46	-	nuc	0	Cytoplasm (By similarity)				269
Q8C503 UniProt NPD GO	SIT1_MOUSE	Signaling threshold-regulating transmembrane adapter 1 (Suppression-inducing transmembrane adapter 1 ...	0.46	-	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity)				180
Q00445 UniProt NPD GO	HS21C_WHEAT	Small heat shock protein, chloroplast precursor (Heat shock protein 26.6)	0.46	-	mit	0	Plastid; chloroplast				238
Q9Z1X0 UniProt NPD GO	CCL27_MOUSE	Small inducible cytokine A27 precursor (CCL27) (CC chemokine ILC) (IL-11 R-alpha-locus chemokine) (m ...	0.46	-	nuc	0	Isoform 1: Secreted protein. Nucleus. Isoform 1 may also be nuclear when following receptor (CCR10)- ...				120
Q07325 UniProt NPD GO	SCYB9_HUMAN	Small inducible cytokine B9 precursor (CXCL9) (Gamma interferon-induced monokine) (MIG)	0.46	-	nuc	1 *	Secreted protein	extracellular space [TAS]	601704		125
Q91924 UniProt NPD GO	SLUG_XENLA	Snail protein homolog Slug (xSlu)	0.46	-	nuc	0	Nucleus (Probable)				266
Q90216 UniProt NPD GO	SOML_ANGAN	Somatolactin precursor (SL)	0.46	-	mit	0	Secreted protein				228
Q9I9M4 UniProt NPD GO	SOMA_PSECR	Somatotropin precursor (Growth hormone)	0.46	-	exc	0	Secreted protein				204
Q75C43 UniProt NPD GO	SNX4_ASHGO	Sorting nexin-4 (Autophagy-related protein 24)	0.46	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				410
Q9BXN6 UniProt NPD GO	SPNXD_HUMAN	Sperm protein associated with the nucleus on the X chromosome D (Nuclear-associated protein SPAN-Xd) ...	0.46	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Associated with nuclear craters (By similarity)				97
O43120 UniProt NPD GO	UAP2_SCHPO	Splicing factor U2AF-associated protein 2	0.46	-	cyt	0		snRNP U2 [IPI]			367
Q04921 UniProt NPD GO	SPR28_YEAST	Sporulation-regulated protein 28	0.46	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Bud neck (By similarity). Present at the bud ...	septin ring (sensu Saccharomyces) [TAS]			423
Q9PTL2 UniProt NPD GO	SPY2_CHICK	Sprouty homolog 2 (Spry-2)	0.46	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in the cytoplasm in unstimulated cells but i ...				313
Q66JG9 UniProt NPD GO	SPRE1_XENTR	Sprouty-related, EVH1 domain-containing protein 1 (Spred-1)	0.46	-	nuc	0	Membrane; peripheral membrane protein (By similarity)			1XOD	406
P18301 UniProt NPD GO	STC_ANGAU	Stanniocalcin precursor (STC) (Corpuscles of Stannius protein) (CS) (Hypocalcin) (Teleocalcin)	0.46	-	exc	0					250
Q8VIM6 UniProt NPD GO	STRC_MOUSE	Stereocilin precursor	0.46	-	vac	0	Cell surface. Associated with the hair bundle				1809
P97826 UniProt NPD GO	STAR_RAT	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.46	-	mit	0	Mitochondrion				284
O14543 UniProt NPD GO	SOCS3_HUMAN	Suppressor of cytokine signaling 3 (SOCS-3) (Cytokine-inducible SH2 protein 3) (CIS-3) (STAT-induced ...	0.46	-	nuc	0			604176		225
Q15528 UniProt NPD GO	SURF5_HUMAN	Surfeit locus protein 5	0.46	-	nuc	0		cytoplasm [TAS] mediator complex [IDA] soluble fraction [TAS]	185641		200
Q5R5K4 UniProt NPD GO	SNP29_PONPY	Synaptosomal-associated protein 29 (SNAP-29) (Vesicle-membrane fusion protein SNAP-29) (Soluble 29 k ...	0.46	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Appears to be mostly membrane-bound, probably via ...				258
Q5T7P8 UniProt NPD GO	SYT6_HUMAN	Synaptotagmin-6 (Synaptotagmin VI) (SytVI)	0.46	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)		607718		510
Q9NVN3 UniProt NPD GO	RIC8B_HUMAN	Synembryn-B (Brain synembrin) (hSyn) (Protein Ric-8B)	0.46	-	cyt	0	Cytoplasm; cell cortex. Localizes to the cell cortex		609147		536
Q9Z158 UniProt NPD GO	STX17_RAT	Syntaxin-17	0.46	-	mit	2	Membrane; single-pass type IV membrane protein. Appears to be associated with a membrane compartment ...	endoplasmic reticulum [IDA]			301
O04378 UniProt NPD GO	SYP23_ARATH	Syntaxin-23 (AtSYP23) (AtPLP) (AtPEP12-like protein)	0.46	-	nuc	0	Membrane; single-pass type IV membrane protein. In cv. RLD, probably a type IV membrane protein. Mem ...				255
Q5ZL19 UniProt NPD GO	STX6_CHICK	Syntaxin-6	0.46	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	early endosome [ISS] perinuclear region [ISS]			254
O70257 UniProt NPD GO	STX7_RAT	Syntaxin-7	0.46	-	nuc	1	Endosome; early endosome; early endosomal membrane; single-pass type IV membrane protein (By similar ...	endosome [IDA] integral to membrane [IDA]			260
Q9UL17 UniProt NPD GO	TBX21_HUMAN	T-box transcription factor TBX21 (T-box protein 21) (Transcription factor TBLYM) (T-cell-specific T- ...	0.46	+	nuc	0	Nucleus	nucleus [NAS]	604895		535
P06333 UniProt NPD GO	TCB1_RABIT	T-cell receptor beta chain ANA 11	0.46	-	nuc	1					319
P24161 UniProt NPD GO	CD3Z_MOUSE	T-cell surface glycoprotein CD3 zeta chain precursor (T-cell receptor T3 zeta chain)	0.46	-	end	1 *	Membrane; single-pass type I membrane protein	alpha-beta T cell receptor complex [IDA]			164
Q8R3D1 UniProt NPD GO	TBC13_MOUSE	TBC1 domain family member 13	0.46	-	nuc	0					400
Q8IYX1 UniProt NPD GO	TBC21_HUMAN	TBC1 domain family member 21	0.46	-	cyt	0					336
Q5XJA0 UniProt NPD GO	TTRAP_BRARE	TRAF and TNF receptor-associated protein homolog	0.46	+	nuc	0	Nucleus (By similarity)				369
Q5RD69 UniProt NPD GO	TICN3_PONPY	Testican-3 precursor (SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 3)	0.46	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				436
Q9D411 UniProt NPD GO	TSSK4_MOUSE	Testis-specific serine/threonine-protein kinase 4 (EC 2.7.11.1) (TSSK-4) (Testis-specific kinase 4) ...	0.46	-	cyt	0					328
Q6DKK2 UniProt NPD GO	TTC19_HUMAN	Tetratricopeptide repeat protein 19 (TPR repeat protein 19)	0.46	-	mit	0					380
Q86TV6 UniProt NPD GO	TTC7B_HUMAN	Tetratricopeptide repeat protein 7B (Tetratricopeptide repeat protein 7-like-1)	0.46	-	nuc	0					741

You are viewing entries 27951 to 28000 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.